Alignments for a candidate for mmsA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Klebsiella michiganensis M5al

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate BWI76_RS03070 BWI76_RS03070 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= reanno::Koxy:BWI76_RS03070
         (501 letters)



>FitnessBrowser__Koxy:BWI76_RS03070
          Length = 501

 Score = 1006 bits (2600), Expect = 0.0
 Identities = 501/501 (100%), Positives = 501/501 (100%)

Query: 1   MTITGNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRT 60
           MTITGNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRT
Sbjct: 1   MTITGNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRT 60

Query: 61  TPLRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIK 120
           TPLRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIK
Sbjct: 61  TPLRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIK 120

Query: 121 GEFSSDVGTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSFVLKPPALAPT 180
           GEFSSDVGTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSFVLKPPALAPT
Sbjct: 121 GEFSSDVGTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSFVLKPPALAPT 180

Query: 181 AAVRLAELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRIAAVSFVGSSGVAEHIYKTASAY 240
           AAVRLAELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRIAAVSFVGSSGVAEHIYKTASAY
Sbjct: 181 AAVRLAELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRIAAVSFVGSSGVAEHIYKTASAY 240

Query: 241 GKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIA 300
           GKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIA
Sbjct: 241 GKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIA 300

Query: 301 RLKPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVP 360
           RLKPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVP
Sbjct: 301 RLKPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVP 360

Query: 361 GFEEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFT 420
           GFEEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFT
Sbjct: 361 GFEEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFT 420

Query: 421 SNGHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKT 480
           SNGHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKT
Sbjct: 421 SNGHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKT 480

Query: 481 ATVRWPQGQQTVSEFSMPTLG 501
           ATVRWPQGQQTVSEFSMPTLG
Sbjct: 481 ATVRWPQGQQTVSEFSMPTLG 501


Lambda     K      H
   0.319    0.135    0.404 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 980
Number of extensions: 20
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 501
Length of database: 501
Length adjustment: 34
Effective length of query: 467
Effective length of database: 467
Effective search space:   218089
Effective search space used:   218089
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate BWI76_RS03070 BWI76_RS03070 (methylmalonate-semialdehyde dehydrogenase (CoA acylating))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01722.hmm
# target sequence database:        /tmp/gapView.23184.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.3e-195  636.6   1.1   1.5e-195  636.4   1.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS03070  BWI76_RS03070 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS03070  BWI76_RS03070 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  636.4   1.1  1.5e-195  1.5e-195       3     477 .]       6     485 ..       4     485 .. 0.98

  Alignments for each domain:
  == domain 1  score: 636.4 bits;  conditional E-value: 1.5e-195
                               TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                              +i+Gk+v + s+k +pv +pat++v+ +v+ ++a+ev  a+  ar++f +w+ t+ ++rarv++ ++ ll
  lcl|FitnessBrowser__Koxy:BWI76_RS03070   6 NFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRTTPLRRARVMFNFKMLL 76 
                                             59********************************************************************* PP

                               TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGit 144
                                             ++h +e+a +i++e+Gk+++da G++ rG+evve+ac+++ l++Ge +++v + vd ys+ qplGvvaGit
  lcl|FitnessBrowser__Koxy:BWI76_RS03070  77 EQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIKGEFSSDVGTGVDSYSLMQPLGVVAGIT 147
                                             *********************************************************************** PP

                               TIGR01722 145 pfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdv 215
                                             pfnfpam+p+wmfpla+acGn+fvlkp    p+aav+laell+eaG+pdGv+nvvh  +e  ++l   p +
  lcl|FitnessBrowser__Koxy:BWI76_RS03070 148 PFNFPAMVPMWMFPLALACGNSFVLKPPALAPTAAVRLAELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRI 218
                                             *********************************************************************** PP

                               TIGR01722 216 kavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavl 286
                                              avsfvGs+ v+e+iy+t+sa gkrvqa++ aknh++v+pdad++a+++a++g a+G+aG+rcma+ ++v+
  lcl|FitnessBrowser__Koxy:BWI76_RS03070 219 AAVSFVGSSGVAEHIYKTASAYGKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVA 289
                                             *********************************************************************** PP

                               TIGR01722 287 vGaa..kelveeireraekvrvgagddpg...aelGplitkqakervasliasgakeGaevlldGrgykve 352
                                             vG+   ++l+ +++  +e ++vg+g   g    e+Gp++++ ++++v  +i++g+ eGa +++dGr  +v 
  lcl|FitnessBrowser__Koxy:BWI76_RS03070 290 VGDEtaDKLIARLKPLVESLKVGPGCMRGkeeNEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVP 360
                                             **74459*****************9765522278************************************* PP

                               TIGR01722 353 GyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqh 423
                                             G+eeG +vG tl+++v p+m+i++eeifGpvl ++++  ++ a++l+n   +GnG+a+fts+G +ar+f h
  lcl|FitnessBrowser__Koxy:BWI76_RS03070 361 GFEEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFTSNGHTAREFVH 431
                                             *********************************************************************** PP

                               TIGR01722 424 eievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                             ++++G+vGvnvp+pvp++f+sf+Gwk s+fG l+++G +Gvrfytr+kt t rw
  lcl|FitnessBrowser__Koxy:BWI76_RS03070 432 DVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKTATVRW 485
                                             ****************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (501 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.25
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources